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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagaagatactttttttttaatcctgctggtttcgactaacgtcgccgtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCAAAAGAAAGTCATTGAAGCCAAAAAGACACAGATGCCTGTGAATGTTGCC

Basic information

species Selaginella moellendorffii
transcript EFJ07706
intron # 6
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169065499|gb|FE475857.1|FE475857
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169070025|gb|FE476494.1|FE476494
EST:     GACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: GACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169057396|gb|FE465700.1|FE465700
EST:     GCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: GCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169019341|gb|FE427651.1|FE427651
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169059367|gb|FE467509.1|FE467509
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACACCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169029314|gb|FE439442.1|FE439442
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169070026|gb|FE476495.1|FE476495
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169019340|gb|FE427650.1|FE427650
EST:     CCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169050567|gb|FE459635.1|FE459635
EST:     CCAACTCCTCTTCNTGCTTTAAGAGTCAAGGAAACACCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169038570|gb|FE446895.1|FE446895
EST:     ACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: ACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169051157|gb|FE458691.1|FE458691
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACACCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCANGCACGGACTTGGGACAACTGCTTTCTC
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTC
EST: gi|169114973|gb|FE516338.1|FE516338
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACACCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169111537|gb|FE510397.1|FE510397
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAAC                         GTATCAACAA-TTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
EST: gi|169114972|gb|FE516337.1|FE516337
EST:     CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACACCGACAGAATCAAC                         GTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA
genomic: CCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 26

ACGATGAGCCCGTTGATACGATTTTGCAACGTTTTGTGGAGCTGGGAATTCCAACTCCTCTTCCTGCTTTAAGAGTCAAGGAAACTCCGACAGAATCAACgtatagaaga ... gtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCAAAAGAAAGTCATTGAAGCCAAAAAGACACAGATGCCTGTGAATGTTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagatactttttttttaatcctgctggtttcgactaacgtcgccgtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCAAAAGAAAGTCATTGAAGCCAAAAAGACACAGATGCCTGTGAATGTTGCC
                                gactaac  putative branch site (score: 26)
     tactttttttttaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagaagatactttttttttaatcctgctggtttcgactaacgtcgccgtatatgcagGTATCAACAATTTGAAGAAGCAGGCACGGACTTGGGACAACTGCTTTCTCAAAAGAAAGTCATTGAAGCCAAAAAGACACAGATGCCTGTGAATGTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG